By Kristin Sainani, PhD, and Katharine Miller

Rick Russell, PhD, associate professor of chemistry and biochemistry at the University of Texas, Austin, studies RNA structure formation in the laboratory. Recognizing that his experimental data were not sufficient to give a structural picture of RNA folding, he decided to turn to modeling for help. Last winter, he asked graduate student Yaqi Wan to scour the Internet for RNA modeling tools. She tried for a few weeks but found nothing that was user-friendly enough for a graduate student without training.

Since then, Wan has learned how to use RNABuilder and is helping Flores add functionality to the software—allowing it to model RNAs based on homology to related RNAs. “That hadn’t been done before with RNABuilder and really hadn’t been done much for RNA at all,” says Russell. Russell and Wan then successfully used this new capability on a test case, generating a model of a fairly complex, 200-nucleotide RNA without reference to the known crystal structure. They plan to use RNABuilder to model a related RNA for which the structure of extensive regions is unknown.

“This is basically a first for my lab, to work with computational models,” Russell says. “It's quite helpful to have such knowledgeable and interactive collaborators.”